csd3
The system
1. System
2. Policies
3. Login
4. Directories
5. email
6. Local web browsing
7. Languages
8. Software
9. ceuadmin
10. Parallel Computing
11. QEMU
12. SRCP
13. Green Algorithms
14. A. Setup of modules
15. Training
16. Contacts
17. Acknowledgement
/systems/files/
Python packages
1. gwas2vcf
2. GWAS Catalog
3. ldsc
4. PhySO
5. Scikit-LLM & OpenAI API
6. snakemake
7. Synapse
R packages
1. brms
2. conquer
3. DescTools
4. EasyQC
5. geometries
6. gifski
7. git2r
8. glmnet
9. gnn
10. gsl
11. igraph
12. jqr
13. LDlinkR
14. lpsymphony
15. magick
16. METRO
17. nloptr
18. PhenoScanner
19. PKI
20. plumber
21. protolite
22. rawrr
23. RcppTOML
24. Rfast
25. rgdal
26. rgeos
27. rgl
28. Rhdf5lib
29. rjags
30. rJava
31. RMariaDB
32. rstan
33. rtracklayer
34. SAIGE
35. sf
36. snpnet
37. sojo
38. SPACox
39. tenXplore
40. xlsx
Applications
1. ABCtoolbox
2. AEGIS
3. akt
4. ANNOVAR
5. aria2
6. bcftools
7. bedops
8. bgenix
9. CaVEMaN
10. CAVIAR/eCAVIAR
11. circos
12. citeproc
13. CookHLA
14. Cytoscape
15. DNAnexus
16. DosageConverter
17. finemap
18. GATK
19. GCTA
20. geany
21. Genotype-Harmonizer
22. gsutil
23. hail
24. HESS
25. KentUtils
26. lapack
27. LEMMA
28. LocusZoom
29. METAL
30. MetaXcan
31. pandoc
32. PCA projection
33. peer
34. pgsc_calc
35. PLINK
36. polyphen-2
37. poppler
38. PRSice
39. PRSoS
40. pspp
41. AlphaPept and PyOpenMS
42. qpdf
43. qtltools
44. quarto
45. regenie
46. R
47. RStudio
48. Rust
49. shapeit
50. SMR
51. snipar
52. SNPTEST
53. sra-tools
54. SurvivalGWAS_SV
55. tabix
56. VEP
57. Visual Studio code
58. B. Notes on emsembl-vep
/applications/files/
/applications/files/examples/
cardio
csd3
systems
policies.md
Policies
See
https://docs.hpc.cam.ac.uk/hpc/user-guide/policies.html#acknowledging-csd3
.
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2019-2024,
cambridge-ceu
Revision
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